Citation and License

BMC Bioinformatics 2009, 10:48
doi:10.1186/1471-2105-10-48

Published: 3 February 2009

Abstract

Background

Since the inception of the GO annotation project, a variety of tools have been developed
that support exploring and searching the GO database. In particular, a variety of
tools that perform GO enrichment analysis are currently available. Most of these tools
require as input a target set of genes and a background set and seek enrichment in
the target set compared to the background set. A few tools also exist that support
analyzing ranked lists. The latter typically rely on simulations or on union-bound
correction for assigning statistical significance to the results.

Results

GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes,
without requiring the user to provide explicit target and background sets. This is
particularly useful in many typical cases where genomic data may be naturally represented
as a ranked list of genes (e.g. by level of expression or of differential expression).
GOrilla employs a flexible threshold statistical approach to discover GO terms that are significantly
enriched at the top of a ranked gene list. Building on a complete theoretical characterization of the
underlying distribution, called mHG, GOrilla computes an exact p-value for the observed enrichment, taking threshold multiple testing
into account without the need for simulations. This enables rigorous statistical analysis
of thousand of genes and thousands of GO terms in order of seconds. The output of
the enrichment analysis is visualized as a hierarchical structure, providing a clear
view of the relations between enriched GO terms.

Conclusion

GOrilla is an efficient GO analysis tool with unique features that make a useful addition
to the existing repertoire of GO enrichment tools. GOrilla's unique features and advantages over other threshold free enrichment tools include
rigorous statistics, fast running time and an effective graphical representation.
GOrilla is publicly available at: http://cbl-gorilla.cs.technion.ac.ilwebcite